Could use Text::Table for the output. Using an array of arrays, (also could use hash of arrays with a few adjustments to the code).

#!/usr/bin/perl
use strict;
use warnings;
use Text::Table;
use List::Util 'max';

my @final = (
          [
            'Line_1_3',
            'Line_2_3'
          ],
          [
            'Line_3_3'
          ],
          [
            'Line_4_3',
            'Line_5_3',
            'Line_6_3',
            'Line_7_3'
          ]
        );



my $max_idx = max map $#$_, @final;

my $tb = Text::Table->new;

for my $i (0 .. $max_idx) {
    $tb->add( map $final[$_][$i], 0 .. $#final);
}
print $tb
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The hash method.

#!/usr/bin/perl
use strict;
use warnings;
use Text::Table;
use List::Util 'max';

my %final = (
  'sample.txt' => [
    'Line_1_3long',
    'Line_2_3'
  ],
  'sample_2.txt' => [
    'Line_3_3longer'
  ],
  'sample_3.txt' => [
    'Line_4_3',
    'Line_5_3',
    'Line_6_3evenlonger',
    'Line_7_3',
  ]
);



my $max_idx = max map $#$_, values %final;

my $tb = Text::Table->new;

for my $i (0 .. $max_idx) {
    $tb->add( map $final{$_}[$i], sort keys %final);
}
print $tb
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